Understanding the Plot
- Track 1 (Gene Quality): Shows genes colored by assembly quality
- Green (Excellent): ≥95% identity
- Yellow (Good): 85-95% identity
- Orange (Fair): 70-85% identity
- Red (Poor): <70% identity
- Track 2 (Contig Mapping): Shows which assembly contigs map to the reference
- Track 3 (Coverage Depth): Shows how many times each position is covered
- Track 4 (Alignment Identity): Shows sequence identity percentage across the genome
- Track 5 (Misassemblies): Highlights regions with assembly errors
- Bottom layer: Contig positions (colored bars showing which contig)
- Upper layers: Overlaps, Gaps, and Inversions
Interactive Features
- Click on genes in Track 1 to view detailed alignments
- Hover over any element to see detailed information
- Zoom: Click and drag to select a region, double-click to reset
- Pan: Use the pan tool in the toolbar